There typically are several methods for developing biological reaction systems for diagnostic and therapeutic purposes. A large industry has developed which is involved in the isolation, identification, purification development and production of naturally occurring compounds.
For many years efforts have been directed to the development of therapeutic or diagnostic reagents which are based purely on trial and error experimentation. On the other end of the research spectrum from this approach is to model or "design" therapeutic or diagnostic agents. This is possible due to the abundance of biological information that is now available on the molecular level. Since the advent of AIDS the search for better approaches has increased.
A series of U.S. patents have been issued that describe a modeling method for utilization in bimolecular reaction. See, e.g., U.S. Pat. No. 4,939,666 of Hardman, and U.S. Pat. Nos. 4,946,778; 4,908,773; 4,881,175; 4,8532,871; and 4,704,692. The '666 patent of Hardman describes what is known as the CHARMM model.
The differences between the present invention and CHARMM rest on how the dynamics of molecules are generated. CHARMM and analogous systems, apply Langevin Dynamis and Stochastic Boundary Dynamis or similar methods to predict the motions of molecules. These principles, and the equation used to simulate these principles, apparently assume the environment of a molecule randomly haphazardly disturbs that molecule.
In the present invention the premise for biological systems is that the environment of a molecule precisely and very specifically may interact with the given molecule. The bit transfer mapping scheme is based on empirical experimental data to characterize the motions of molecule. The specific set of biochemical events are identified and it is assumed that the relevant stable elementary particle that transfers during a given chemical reaction, such as the redox event, induces the dynamic of a molecules reaction.